I recently moved by one time zone and I discovered that this messed up the times of events in the Thunderbird calendar (i.e. Lightning). That is, if I create new events (!) and set up warnings for them, I get the warnings one hour too late. After some searching, I discovered that Thunderbird had its very own timezone setting, under Tools - Options - Calendar - Timezone. This was still set to my previous location and solved the problem.

However, I STRONGLY believe that Thunderbird should NOT have a private timezone setting. This is something which should be handled by the operating system! It is bad style to store the timezone in two places and leads to problems as above, which is why I classify this as a bug.